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Cooperative assembly of a four-molecule signaling complex formed upon T cell antigen receptor activation. Proc Natl Acad Sci U S A 2018; 115:E11914-E11923. [PMID: 30510001 DOI: 10.1073/pnas.1817142115] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The T cell antigen receptor encounters foreign antigen during the immune response. Receptor engagement leads to activation of specific protein tyrosine kinases, which then phosphorylate multiple enzymes and adapter proteins. One such enzyme, phospholipase-Cγ1, is responsible for cleavage of a plasma membrane lipid substrate, a phosphoinositide, into two second messengers, diacylglycerol, which activates several enzymes including protein kinase C, and an inositol phosphate, which induces intracellular calcium elevation. In T cells, phospholipase-Cγ1 is recruited to the plasma membrane as part of a four-protein complex containing three adapter molecules. We have used recombinant proteins and synthetic phosphopeptides to reconstitute this quaternary complex in vitro. Extending biophysical tools to study concurrent interactions of the four protein components, we demonstrated the formation and determined the composition of the quaternary complex using multisignal analytical ultracentrifugation, and we characterized the thermodynamic driving forces of assembly by isothermal calorimetry. We demonstrate that the four proteins reversibly associate in a circular arrangement of binding interfaces, each protein interacting with two others. Three interactions are of high affinity, and the fourth is of low affinity, with the assembly of the quaternary complex exhibiting significant enthalpy-entropy compensation as in an entropic switch. Formation of this protein complex enables subsequent recruitment of additional molecules needed to activate phospholipase-Cγ1. Understanding the formation of this complex is fundamental to full characterization of a central pathway in T cell activation. Such knowledge is critical to developing ways in which this pathway can be selectively inhibited.
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102
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Zhu X, Poghosyan E, Rezabkova L, Mehall B, Sakakibara H, Hirono M, Kamiya R, Ishikawa T, Yang P. The roles of a flagellar HSP40 ensuring rhythmic beating. Mol Biol Cell 2018; 30:228-241. [PMID: 30427757 PMCID: PMC6589562 DOI: 10.1091/mbc.e18-01-0047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
HSP40s are regarded as cochaperones, perpetually shuttling client polypeptides to HSP70s for refolding. However, many HSP40s that are central for disparate processes diverge from this paradigm. To elucidate the noncanonical mechanisms, we investigated HSP40 in the radial spoke (RS) complex in flagella. Disruption of the gene by the MRC1 transposon in Chlamydomonas resulted in jerky flagella. Traditional electron microscopy, cryo-electron tomography, and sub-tomogram analysis revealed RSs of various altered morphologies that, unexpectedly, differed between the two RS species. This indicates that HSP40 locks the RS into a functionally rigid conformation, facilitating its interactions with the adjacent central pair apparatus for transducing locally varied mechanical feedback, which permits rhythmic beating. Missing HSP40, like missing RSs, could be restored in a tip-to-base direction when HSP40 mutants fused with a HSP40 donor cell. However, without concomitant de novo RS assembly, the repair was exceedingly slow, suggesting HSP40/RS-coupled intraflagellar trafficking and assembly. Biochemical analysis and modeling uncovered spoke HSP40’s cochaperone traits. On the basis of our data, we propose that HSP40 accompanies its client RS precursor when traveling to the flagellar tip. Upon arrival, both refold in concert to assemble into the mature configuration. HSP40’s roles in chaperoning and structural maintenance shed new light on its versatility and flagellar biology.
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Affiliation(s)
- Xiaoyan Zhu
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233
| | - Emiliya Poghosyan
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Lenka Rezabkova
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Bridget Mehall
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233
| | - Hitoshi Sakakibara
- National Institute of Information and Communications Technology (NICT), Advanced ICT Research Institute, Hyogo 651-2492, Japan
| | - Masafumi Hirono
- Department of Frontier Bioscience, Hosei University, Tokyo 184-8584, Japan
| | - Ritsu Kamiya
- Department of Life Science, Faculty of Science, Gakushuin University, Tokyo 171-8588, Japan
| | - Takashi Ishikawa
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Pinfen Yang
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233
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103
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Keul ND, Oruganty K, Schaper Bergman ET, Beattie NR, McDonald WE, Kadirvelraj R, Gross ML, Phillips RS, Harvey SC, Wood ZA. The entropic force generated by intrinsically disordered segments tunes protein function. Nature 2018; 563:584-588. [PMID: 30420606 PMCID: PMC6415545 DOI: 10.1038/s41586-018-0699-5] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 09/10/2018] [Indexed: 11/09/2022]
Abstract
Protein structures are dynamic and can explore a large conformational landscape1,2. Only some of these structural substates are important for protein function (such as ligand binding, catalysis and regulation)3-5. How evolution shapes the structural ensemble to optimize a specific function is poorly understood3,4. One of the constraints on the evolution of proteins is the stability of the folded 'native' state. Despite this, 44% of the human proteome contains intrinsically disordered peptide segments greater than 30 residues in length6, the majority of which have no known function7-9. Here we show that the entropic force produced by an intrinsically disordered carboxy terminus (ID-tail) shifts the conformational ensemble of human UDP-α-D-glucose-6-dehydrogenase (UGDH) towards a substate with a high affinity for an allosteric inhibitor. The function of the ID-tail does not depend on its sequence or chemical composition. Instead, the affinity enhancement can be accurately predicted based on the length of the intrinsically disordered segment, and is consistent with the entropic force generated by an unstructured peptide attached to the protein surface10-13. Our data show that the unfolded state of the ID-tail rectifies the dynamics and structure of UGDH to favour inhibitor binding. Because this entropic rectifier does not have any sequence or structural constraints, it is an easily acquired adaptation. This model implies that evolution selects for disordered segments to tune the energy landscape of proteins, which may explain the persistence of intrinsic disorder in the proteome.
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Affiliation(s)
- Nicholas D Keul
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Krishnadev Oruganty
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | | | - Nathaniel R Beattie
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Weston E McDonald
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Renuka Kadirvelraj
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Stephen C Harvey
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Zachary A Wood
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
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104
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Shi Y, Hong X, Fan H, Wu Z, Liu A. Characterizing Novel Modifications of a Therapeutic Protein Using Ultra Performance Liquid Chromatography-Tandem Mass Spectrometry, Sedimentation Velocity Analytical Ultracentrifugation, and Structural Modeling. Anal Chem 2018; 90:12870-12877. [PMID: 30295031 DOI: 10.1021/acs.analchem.8b03459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Heterogeneity of biopharmaceutical products is common due to various co- and post-translational modifications and degradation events that occur during the biological production process and throughout the shelf life. Product-related variants resulting from these modifications potentially affect a product's biological activity and safety, and thus, their detailed structure characterization is of great importance for successful development of protein therapeutics. Specifically, in this study, two novel low-level product variants in a recombinant therapeutic protein were characterized via chromatographic enrichment followed by proteolytic digestion and analysis using ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). One of the variants was identified to be the therapeutic protein missing a 61-amino-acid fragment from its N-terminus. Consequently, the other variant was found to be the therapeutic protein carrying the 61-amino-acid long peptide. Furthermore, detailed structure at the modification site of the latter variant was determined as that amino group from the protein's N-terminus linked to side chain carbonyl carbon at Asp 61 residue of the peptide, based on the complementary information from collision induced dissociation and electron transfer dissociation MS/MS analysis. Results from sedimentation velocity analytical ultracentrifugation and computational structural modeling supported the hypothesis that formation of these two variants was a result of protein self-association. In dimeric state, the head-to-toe stacking conformation of two therapeutic protein molecules allowed spatial closeness between the N-terminus of one molecule and the 61st amino acid of the other molecule, resulting in a novel peptide transfer between the two protein molecules.
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105
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Paf1 and Ctr9 subcomplex formation is essential for Paf1 complex assembly and functional regulation. Nat Commun 2018; 9:3795. [PMID: 30228257 PMCID: PMC6143631 DOI: 10.1038/s41467-018-06237-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 08/15/2018] [Indexed: 11/09/2022] Open
Abstract
The evolutionarily conserved multifunctional polymerase-associated factor 1 (Paf1) complex (Paf1C), which is composed of at least five subunits (Paf1, Leo1, Ctr9, Cdc73, and Rtf1), plays vital roles in gene regulation and has connections to development and human diseases. Here, we report two structures of each of the human and yeast Ctr9/Paf1 subcomplexes, which assemble into heterodimers with very similar conformations, revealing an interface between the tetratricopeptide repeat module in Ctr9 and Paf1. The structure of the Ctr9/Paf1 subcomplex may provide mechanistic explanations for disease-associated mutations in human PAF1 and CTR9. Our study reveals that the formation of the Ctr9/Paf1 heterodimer is required for the assembly of yeast Paf1C, and is essential for yeast viability. In addition, disruption of the interaction between Paf1 and Ctr9 greatly affects the level of histone H3 methylation in vivo. Collectively, our results shed light on Paf1C assembly and functional regulation.
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106
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Abstract
In most bacteria and archaea, filaments of FtsZ protein organize cell division. FtsZ forms a ring structure at the division site and starts the recruitment of 10 to 20 downstream proteins that together form a multiprotein complex termed the divisome. The divisome is thought to facilitate many of the steps required to make two cells out of one. FtsQ and FtsB are part of the divisome, with FtsQ being a central hub, interacting with most of the other divisome components. Here we show for the first time in detail how FtsQ interacts with its downstream partner FtsB and show that mutations that disturb the interface between the two proteins effectively inhibit cell division. Most bacteria and archaea use the tubulin homologue FtsZ as its central organizer of cell division. In Gram-negative Escherichia coli bacteria, FtsZ recruits cytosolic, transmembrane, periplasmic, and outer membrane proteins, assembling the divisome that facilitates bacterial cell division. One such divisome component, FtsQ, a bitopic membrane protein with a globular domain in the periplasm, has been shown to interact with many other divisome proteins. Despite its otherwise unknown function, it has been shown to be a major divisome interaction hub. Here, we investigated the interactions of FtsQ with FtsB and FtsL, two small bitopic membrane proteins that act immediately downstream of FtsQ. We show in biochemical assays that the periplasmic domains of E. coli FtsB and FtsL interact with FtsQ, but not with each other. Our crystal structure of FtsB bound to the β domain of FtsQ shows that only residues 64 to 87 of FtsB interact with FtsQ. A synthetic peptide comprising those 24 FtsB residues recapitulates the FtsQ-FtsB interactions. Protein deletions and structure-guided mutant analyses validate the structure. Furthermore, the same structure-guided mutants show cell division defects in vivo that are consistent with our structure of the FtsQ-FtsB complex that shows their interactions as they occur during cell division. Our work provides intricate details of the interactions within the divisome and also provides a tantalizing view of a highly conserved protein interaction in the periplasm of bacteria that is an excellent target for cell division inhibitor searches.
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107
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Istvan P, Souza AA, Garay AV, Dos Santos DFK, de Oliveira GM, Santana RH, Lopes FAC, de Freitas SM, Barbosa JARG, Krüger RH. Structural and functional characterization of a novel lipolytic enzyme from a Brazilian Cerrado soil metagenomic library. Biotechnol Lett 2018; 40:1395-1406. [PMID: 30062528 DOI: 10.1007/s10529-018-2598-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 07/25/2018] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To isolate putative lipase enzymes by screening a Cerrado soil metagenomic library with novel features. RESULTS Of 6720 clones evaluated, Clone W (10,000 bp) presented lipolytic activity and four predicted coding sequences, one of them LipW. Characterization of a predicted esterase/lipase, LipW, showed 28% sequence identity with an arylesterase from Pseudomonas fluorescens (pdb|3HEA) from protein database (PDB). Phylogenetic analysis showed LipW clustered with family V lipases; however, LipW was clustered in different subclade belonged to family V, suggesting a different subgroup of family V. In addition, LipW presented a difference in family V GH motif, a glycine replaced by a serine in GH motif. Estimated molecular weight and stokes radius values of LipW were 29,338.67-29,411.98 Da and 2.58-2.83 nm, respectively. Optimal enzyme activity was observed at pH 9.0-9.5 and at 40 °C. Circular dichroism analysis estimated secondary structures percentages as approximately 45% α-helix and 15% β-sheet, consistent with the 3D structure predicted by homology. CONCLUSION Our results demonstrate the isolation of novel family V lipolytic enzyme with biotechnological applications from a metagenomic library.
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Affiliation(s)
- Paula Istvan
- Laboratório de Enzimologia, Departamento de Biologia Celular, Instituto Central de Ciências Sul, Universidade de Brasília - UnB, Brasília, DF, 700910-900, Brazil
| | - Amanda Araújo Souza
- Laboratório de Biofísica, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, Brazil
| | - Aisel Valle Garay
- Laboratório de Biofísica, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, Brazil
| | - Debora Farage Knupp Dos Santos
- Laboratório de Enzimologia, Departamento de Biologia Celular, Instituto Central de Ciências Sul, Universidade de Brasília - UnB, Brasília, DF, 700910-900, Brazil
| | - Gideane Mendes de Oliveira
- Laboratório de Biofísica, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, Brazil
| | | | - Fabyano Alvares Cardoso Lopes
- Laboratório de Enzimologia, Departamento de Biologia Celular, Instituto Central de Ciências Sul, Universidade de Brasília - UnB, Brasília, DF, 700910-900, Brazil
| | - Sonia Maria de Freitas
- Laboratório de Biofísica, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, Brazil
| | | | - Ricardo Henrique Krüger
- Laboratório de Enzimologia, Departamento de Biologia Celular, Instituto Central de Ciências Sul, Universidade de Brasília - UnB, Brasília, DF, 700910-900, Brazil.
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108
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McClintock MA, Dix CI, Johnson CM, McLaughlin SH, Maizels RJ, Hoang HT, Bullock SL. RNA-directed activation of cytoplasmic dynein-1 in reconstituted transport RNPs. eLife 2018; 7:36312. [PMID: 29944118 PMCID: PMC6056234 DOI: 10.7554/elife.36312] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/19/2018] [Indexed: 12/19/2022] Open
Abstract
Polarised mRNA transport is a prevalent mechanism for spatial control of protein synthesis. However, the composition of transported ribonucleoprotein particles (RNPs) and the regulation of their movement are poorly understood. We have reconstituted microtubule minus end-directed transport of mRNAs using purified components. A Bicaudal-D (BicD) adaptor protein and the RNA-binding protein Egalitarian (Egl) are sufficient for long-distance mRNA transport by the dynein motor and its accessory complex dynactin, thus defining a minimal transport-competent RNP. Unexpectedly, the RNA is required for robust activation of dynein motility. We show that a cis-acting RNA localisation signal promotes the interaction of Egl with BicD, which licenses the latter protein to recruit dynein and dynactin. Our data support a model for BicD activation based on RNA-induced occupancy of two Egl-binding sites on the BicD dimer. Scaffolding of adaptor protein assemblies by cargoes is an attractive mechanism for regulating intracellular transport. In our cells, tiny molecular motors transport the components necessary for life’s biological processes from one location to another. They do so by loading their cargo, and burning up chemical fuel to carry it along pathways made of filaments. For example, one such motor, called dynein, can move molecules of messenger RNA (mRNA) to specific locations within the cell. There, the mRNA will be used as a template to create proteins, which will operate at exactly the right place. Transporting mRNA in this way is critical in processes such as embryonic development and the formation of memories; yet, this mechanism is still poorly understood. Previous work suggested that the mRNA is simply a passenger of the dynein motor, but McClintock et al. asked if this is really the case. Instead, could mRNA regulate its own sorting by controlling the activity of dynein? Studying mRNA trafficking within the complex molecular environment of a cell is challenging, so mRNA transporting machinery was recreated in the laboratory. Only the proteins necessary to build a working system were included in the experiments. In addition to the filaments, the components included dynein and a complex of proteins known as dynactin, which allows the motor to move together with a protein called BICD2. A protein named Egalitarian was used to link the mRNA to BICD2. By filming fluorescently labelled proteins and mRNAs, McClintock et al. discovered that mRNA strongly promotes the movement of the dynein motor. A structured section in the mRNA acts as a docking area for two copies of Egalitarian. This activates BICD2, which then binds to dynein and dynactin, thereby completing the transport machinery. According to these results, the mRNA directs the assembly of the system that will carry it within the cell. Viruses such as HIV and herpesvirus hijack dynein motors to have their genetic information moved around a cell in order to propagate infection. Understanding precisely how mRNA is transported may help to develop new strategies to fight these viruses.
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Affiliation(s)
- Mark A McClintock
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Carly I Dix
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Christopher M Johnson
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Stephen H McLaughlin
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Rory J Maizels
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Ha Thi Hoang
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Simon L Bullock
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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109
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Meier M, Moya-Torres A, Krahn NJ, McDougall MD, Orriss GL, McRae EK, Booy EP, McEleney K, Patel TR, McKenna SA, Stetefeld J. Structure and hydrodynamics of a DNA G-quadruplex with a cytosine bulge. Nucleic Acids Res 2018; 46:5319-5331. [PMID: 29718405 PMCID: PMC6007744 DOI: 10.1093/nar/gky307] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 04/05/2018] [Accepted: 04/12/2018] [Indexed: 12/27/2022] Open
Abstract
The identification of four-stranded G-quadruplexes (G4s) has highlighted the fact that DNA has additional spatial organisations at its disposal other than double-stranded helices. Recently, it became clear that the formation of G4s is not limited to the traditional G3+NL1G3+NL2G3+NL3G3+ sequence motif. Instead, the G3 triplets can be interrupted by deoxythymidylate (DNA) or uridylate (RNA) where the base forms a bulge that loops out from the G-quadruplex core. Here, we report the first high-resolution X-ray structure of a unique unimolecular DNA G4 with a cytosine bulge. The G4 forms a dimer that is stacked via its 5'-tetrads. Analytical ultracentrifugation, static light scattering and small angle X-ray scattering confirmed that the G4 adapts a predominantly dimeric structure in solution. We provide a comprehensive comparison of previously published G4 structures containing bulges and report a special γ torsion angle range preferentially populated by the G4 core guanylates adjacent to bulges. Since the penalty for introducing bulges appears to be negligible, it should be possible to functionalize G4s by introducing artificial or modified nucleotides at such positions. The presence of the bulge alters the surface of the DNA, providing an opportunity to develop drugs that can specifically target individual G4s.
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Affiliation(s)
- Markus Meier
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Aniel Moya-Torres
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Natalie J Krahn
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Matthew D McDougall
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - George L Orriss
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Ewan K S McRae
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Evan P Booy
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Kevin McEleney
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Trushar R Patel
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
- DiscoveryLab, Medical Sciences Building, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary T2N 1N4, Alberta, Canada
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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Komárek J, Ivanov Kavková E, Houser J, Horáčková A, Ždánská J, Demo G, Wimmerová M. Structure and properties of AB21, a novelAgaricus bisporusprotein with structural relation to bacterial pore-forming toxins. Proteins 2018; 86:897-911. [DOI: 10.1002/prot.25522] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/23/2018] [Accepted: 04/26/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Jan Komárek
- Central European Institute of Technology, Masaryk University, Kamenice 5; Brno 62500 Czech Republic
- National Centre for Biomolecular Research; Faculty of Science, Masaryk University, Kotlarska 2; Brno 61137 Czech Republic
| | - Eva Ivanov Kavková
- Department of Biochemistry; Faculty of Science, Masaryk University, Kotlarska 2; Brno 61137 Czech Republic
| | - Josef Houser
- Central European Institute of Technology, Masaryk University, Kamenice 5; Brno 62500 Czech Republic
- National Centre for Biomolecular Research; Faculty of Science, Masaryk University, Kotlarska 2; Brno 61137 Czech Republic
| | - Aneta Horáčková
- Department of Biochemistry; Faculty of Science, Masaryk University, Kotlarska 2; Brno 61137 Czech Republic
| | - Jitka Ždánská
- Central European Institute of Technology, Masaryk University, Kamenice 5; Brno 62500 Czech Republic
| | - Gabriel Demo
- Central European Institute of Technology, Masaryk University, Kamenice 5; Brno 62500 Czech Republic
- National Centre for Biomolecular Research; Faculty of Science, Masaryk University, Kotlarska 2; Brno 61137 Czech Republic
| | - Michaela Wimmerová
- Central European Institute of Technology, Masaryk University, Kamenice 5; Brno 62500 Czech Republic
- National Centre for Biomolecular Research; Faculty of Science, Masaryk University, Kotlarska 2; Brno 61137 Czech Republic
- Department of Biochemistry; Faculty of Science, Masaryk University, Kotlarska 2; Brno 61137 Czech Republic
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111
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Lu P, Min D, DiMaio F, Wei KY, Vahey MD, Boyken SE, Chen Z, Fallas JA, Ueda G, Sheffler W, Mulligan VK, Xu W, Bowie JU, Baker D. Accurate computational design of multipass transmembrane proteins. Science 2018; 359:1042-1046. [PMID: 29496880 DOI: 10.1126/science.aaq1739] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 01/11/2018] [Indexed: 01/01/2023]
Abstract
The computational design of transmembrane proteins with more than one membrane-spanning region remains a major challenge. We report the design of transmembrane monomers, homodimers, trimers, and tetramers with 76 to 215 residue subunits containing two to four membrane-spanning regions and up to 860 total residues that adopt the target oligomerization state in detergent solution. The designed proteins localize to the plasma membrane in bacteria and in mammalian cells, and magnetic tweezer unfolding experiments in the membrane indicate that they are very stable. Crystal structures of the designed dimer and tetramer-a rocket-shaped structure with a wide cytoplasmic base that funnels into eight transmembrane helices-are very close to the design models. Our results pave the way for the design of multispan membrane proteins with new functions.
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Affiliation(s)
- Peilong Lu
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Duyoung Min
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, University of California, Los Angeles (UCLA), CA 90095, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Kathy Y Wei
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Michael D Vahey
- Department of Bioengineering and Biophysics Group, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Scott E Boyken
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Zibo Chen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Jorge A Fallas
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - George Ueda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Vikram Khipple Mulligan
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Wenqing Xu
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - James U Bowie
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, University of California, Los Angeles (UCLA), CA 90095, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. .,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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Self-homodimerization of an actinoporin by disulfide bridging reveals implications for their structure and pore formation. Sci Rep 2018; 8:6614. [PMID: 29700324 PMCID: PMC5920107 DOI: 10.1038/s41598-018-24688-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/04/2018] [Indexed: 11/17/2022] Open
Abstract
The Trp111 to Cys mutant of sticholysin I, an actinoporin from Stichodactyla helianthus sea anemone, forms a homodimer via a disulfide bridge. The purified dimer is 193 times less hemolytic than the monomer. Ultracentrifugation, dynamic light scattering and size-exclusion chromatography demonstrate that monomers and dimers are the only independent oligomeric states encountered. Indeed, circular dichroism and fluorescence spectroscopies showed that Trp/Tyr residues participate in homodimerization and that the dimer is less thermostable than the monomer. A homodimer three-dimensional model was constructed and indicates that Trp147/Tyr137 are at the homodimer interface. Spectroscopy results validated the 3D-model and assigned 85° to the disulfide bridge dihedral angle responsible for dimerization. The homodimer model suggests that alterations in the membrane/carbohydrate-binding sites in one of the monomers, as result of dimerization, could explain the decrease in the homodimer ability to form pores.
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113
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Dickson C, Fletcher AJ, Vaysburd M, Yang JC, Mallery DL, Zeng J, Johnson CM, McLaughlin SH, Skehel M, Maslen S, Cruickshank J, Huguenin-Dezot N, Chin JW, Neuhaus D, James LC. Intracellular antibody signalling is regulated by phosphorylation of the Fc receptor TRIM21. eLife 2018; 7:32660. [PMID: 29667579 PMCID: PMC5906095 DOI: 10.7554/elife.32660] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 03/16/2018] [Indexed: 12/18/2022] Open
Abstract
Cell surface Fc receptors activate inflammation and are tightly controlled to prevent autoimmunity. Antibodies also simulate potent immune signalling from inside the cell via the cytosolic antibody receptor TRIM21, but how this is regulated is unknown. Here we show that TRIM21 signalling is constitutively repressed by its B-Box domain and activated by phosphorylation. The B-Box occupies an E2 binding site on the catalytic RING domain by mimicking E2-E3 interactions, inhibiting TRIM21 ubiquitination and preventing immune activation. TRIM21 is derepressed by IKKβ and TBK1 phosphorylation of an LxxIS motif in the RING domain, at the interface with the B-Box. Incorporation of phosphoserine or a phosphomimetic within this motif relieves B-Box inhibition, promoting E2 binding, RING catalysis, NF-κB activation and cytokine transcription upon infection with DNA or RNA viruses. These data explain how intracellular antibody signalling is regulated and reveal that the B-Box is a critical regulator of RING E3 ligase activity. Antibodies are molecules made by the immune system that protect us from infections. They were discovered over 100 years ago, and for most of that time scientists thought they only worked in the bloodstream. Yet recent research showed that when a virus infects our cells it also carries antibodies in with it. Once inside the cell, a protein called TRIM21 recognises the antibody-covered virus and – together with other proteins called ubiquitin enzymes – targets it for destruction via the cell’s waste disposal system. At the same time TRIM21 sends a signal to the cell’s nucleus to activate certain genes that protect cells across the body from subsequent infection. The genes activated by TRIM21 have potent antiviral activity. Yet they can also damage the body’s own tissues if they are switched on at the wrong time, which may lead to autoimmune diseases like rheumatoid arthritis and multiple sclerosis. It is thus critical that TRIM21 is carefully regulated and only activated during an infection, but it was not clear how this is achieved. Dickson, Fletcher et al. now show that although TRIM21 is made all the time and is always ready to detect an incoming virus it is made in an inactive state. This is because part of TRIM21, called a B-Box, inhibits the protein’s own activity. This was an unexpected discovery because, although the B-Box domain is found in around 100 other human proteins, it was unclear what it did. Dickson, Fletcher et al. then combined structural biology and biochemical approaches to show that the B-Box mimics specific enzymes that work with TRIM21, and blocks them from binding to it. This keeps TRIM21 in an inactive state. Next, Dickson, Fletcher et al. discovered that TRIM21 becomes active when a chemical tag, specifically a phosphate group, is added to the protein. This modification displaces the B-Box, allowing ubiquitin enzymes to bind to TRIM21 and switch on its activity. Further experiments then showed that this process helps regulate TRIM21 during infections with different viruses, including rhinovirus – the virus behind the common cold – and adenovirus – a common cause of respiratory infection. Antibodies are now used to treat many medical conditions, but present technologies are based on our understanding of how antibodies work outside cells. By revealing the basis of antibody immunity inside cells, these new findings may lead to new treatments for a range of conditions. Future studies could also explore how failures in the TRIM21 system contribute to autoimmune diseases.
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Affiliation(s)
- Claire Dickson
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Adam J Fletcher
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Marina Vaysburd
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Ji-Chun Yang
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Donna L Mallery
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Jingwei Zeng
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Stephen H McLaughlin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Mark Skehel
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Sarah Maslen
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - James Cruickshank
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - David Neuhaus
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Leo C James
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
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114
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Dada O, Gutowski S, Brautigam CA, Chen Z, Sternweis PC. Direct regulation of p190RhoGEF by activated Rho and Rac GTPases. J Struct Biol 2018; 202:13-24. [PMID: 29196061 PMCID: PMC5835413 DOI: 10.1016/j.jsb.2017.11.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 11/21/2017] [Accepted: 11/27/2017] [Indexed: 12/16/2022]
Abstract
Rho family GTPases regulate a wide range of cellular processes. This includes cellular dynamics where three subfamilies, Rho, Rac, and Cdc42, are known to regulate cell shape and migration though coordinate action. Activation of Rho proteins largely depends on Rho Guanine nucleotide Exchange Factors (RhoGEFs) through a catalytic Dbl homology (DH) domain linked to a pleckstrin homology (PH) domain that subserves various functions. The PH domains from Lbc RhoGEFs, which specifically activate RhoA, have been shown to bind to activated RhoA. Here, p190RhoGEF is shown to also bind Rac1·GTP. Crystal structures reveal that activated Rac1 and RhoA use their effector-binding surfaces to associate with the same hydrophobic surface on the PH domain. Both activated RhoA and Rac1 can stimulate exchange of nucleotide on RhoA by localization of p190RhoGEF to its substrate, RhoA·GDP, in vitro. The binding of activated RhoA provides a mechanism for positive feedback regulation as previously proposed for the family of Lbc RhoGEFs. In contrast, the novel interaction between activated Rac1 and p190RhoGEF reveals a potential mechanism for cross-talk regulation where Rac can directly effect stimulation of RhoA. The greater capacity of Rac1 to stimulate p190RhoGEF among the Lbc RhoGEFs suggests functional specialization.
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Affiliation(s)
- Olugbenga Dada
- Department of Pharmacology, The University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA.
| | - Stephen Gutowski
- Department of Pharmacology, The University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA.
| | - Chad A Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA; Department of Microbiology, The University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA.
| | - Zhe Chen
- Department of Biophysics, The University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA.
| | - Paul C Sternweis
- Department of Pharmacology, The University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA.
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115
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de Jong APH, Roggero CM, Ho MR, Wong MY, Brautigam CA, Rizo J, Kaeser PS. RIM C 2B Domains Target Presynaptic Active Zone Functions to PIP 2-Containing Membranes. Neuron 2018; 98:335-349.e7. [PMID: 29606581 DOI: 10.1016/j.neuron.2018.03.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 02/01/2018] [Accepted: 03/05/2018] [Indexed: 11/16/2022]
Abstract
Rapid and efficient synaptic vesicle fusion requires a pool of primed vesicles, the nearby tethering of Ca2+ channels, and the presence of the phospholipid PIP2 in the target membrane. Although the presynaptic active zone mediates the first two requirements, it is unclear how fusion is targeted to membranes with high PIP2 content. Here we find that the C2B domain of the active zone scaffold RIM is critical for action potential-triggered fusion. Remarkably, the known RIM functions in vesicle priming and Ca2+ influx do not require RIM C2B domains. Instead, biophysical experiments reveal that RIM C2 domains, which lack Ca2+ binding, specifically bind to PIP2. Mutational analyses establish that PIP2 binding to RIM C2B and its tethering to the other RIM domains are crucial for efficient exocytosis. We propose that RIM C2B domains are constitutive PIP2-binding modules that couple mechanisms for vesicle priming and Ca2+ channel tethering to PIP2-containing target membranes.
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Affiliation(s)
- Arthur P H de Jong
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Carlos M Roggero
- Departments of Biophysics, Biochemistry, and Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Meng-Ru Ho
- Departments of Biophysics, Biochemistry, and Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Man Yan Wong
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Chad A Brautigam
- Departments of Biophysics and Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Josep Rizo
- Departments of Biophysics, Biochemistry, and Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Pascal S Kaeser
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.
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116
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Basal condensation of Numb and Pon complex via phase transition during Drosophila neuroblast asymmetric division. Nat Commun 2018; 9:737. [PMID: 29467404 PMCID: PMC5821850 DOI: 10.1038/s41467-018-03077-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 01/17/2018] [Indexed: 12/16/2022] Open
Abstract
Uneven distribution and local concentration of protein complexes on distinct membrane cortices is a fundamental property in numerous biological processes, including Drosophila neuroblast (NB) asymmetric cell divisions and cell polarity in general. In NBs, the cell fate determinant Numb forms a basal crescent together with Pon and is segregated into the basal daughter cell to initiate its differentiation. Here we discover that Numb PTB domain, using two distinct binding surfaces, recognizes repeating motifs within Pon in a previously unrecognized mode. The multivalent Numb-Pon interaction leads to high binding specificity and liquid-liquid phase separation of the complex. Perturbations of the Numb/Pon complex phase transition impair the basal localization of Numb and its subsequent suppression of Notch signaling during NB asymmetric divisions. Such phase-transition-mediated protein condensations on distinct membrane cortices may be a general mechanism for various cell polarity regulatory complexes. Polarized localization of Numb and Pon in Drosophila neuroblasts (NBs) enables their unequal segregation during asymmetric cell divisions. Here, the authors demonstrate liquid-liquid phase separation of Pon and Numb in NBs mediated by multivalent intermolecular interactions is required for their basal condensation.
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117
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Chittori S, Hong J, Saunders H, Feng H, Ghirlando R, Kelly AE, Bai Y, Subramaniam S. Structural mechanisms of centromeric nucleosome recognition by the kinetochore protein CENP-N. Science 2017; 359:339-343. [PMID: 29269420 DOI: 10.1126/science.aar2781] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/12/2017] [Indexed: 11/02/2022]
Abstract
Accurate chromosome segregation requires the proper assembly of kinetochore proteins. A key step in this process is the recognition of the histone H3 variant CENP-A in the centromeric nucleosome by the kinetochore protein CENP-N. We report cryo-electron microscopy (cryo-EM), biophysical, biochemical, and cell biological studies of the interaction between the CENP-A nucleosome and CENP-N. We show that human CENP-N confers binding specificity through interactions with the L1 loop of CENP-A, stabilized by electrostatic interactions with the nucleosomal DNA. Mutational analyses demonstrate analogous interactions in Xenopus, which are further supported by residue-swapping experiments involving the L1 loop of CENP-A. Our results are consistent with the coevolution of CENP-N and CENP-A and establish the structural basis for recognition of the CENP-A nucleosome to enable kinetochore assembly and centromeric chromatin organization.
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Affiliation(s)
- Sagar Chittori
- Laboratory of Cell Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Jingjun Hong
- Laboratory of Biochemistry and Molecular Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Hayden Saunders
- Laboratory of Biochemistry and Molecular Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Hanqiao Feng
- Laboratory of Biochemistry and Molecular Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD 20892, USA
| | - Alexander E Kelly
- Laboratory of Biochemistry and Molecular Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA.
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA.
| | - Sriram Subramaniam
- Laboratory of Cell Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA.
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118
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The Y. bercovieri Anbu crystal structure sheds light on the evolution of highly (pseudo)symmetric multimers. J Mol Biol 2017; 430:611-627. [PMID: 29258816 PMCID: PMC6376114 DOI: 10.1016/j.jmb.2017.11.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/22/2017] [Accepted: 11/09/2017] [Indexed: 12/11/2022]
Abstract
Ancestral β-subunit (Anbu) is homologous to HslV and 20S proteasomes. Based on its phylogenetic distribution and sequence clustering, Anbu has been proposed as the “ancestral” form of proteasomes. Here, we report biochemical data, small-angle X-ray scattering results, negative-stain electron microscopy micrographs and a crystal structure of the Anbu particle from Yersinia bercovieri (YbAnbu). All data are consistent with YbAnbu forming defined 12–14 subunit multimers that differ in shape from both HslV and 20S proteasomes. The crystal structure reveals that YbAnbu subunits form tight dimers, held together in part by the Anbu specific C-terminal helices. These dimers (“protomers”) further assemble into a low-rise left-handed staircase. The lock-washer shape of YbAnbu is consistent with the presence of defined multimers, X-ray diffraction data in solution and negative-stain electron microscopy images. The presented structure suggests a possible evolutionary pathway from helical filaments to highly symmetric or pseudosymmetric multimer structures. YbAnbu subunits have the Ntn-hydrolase fold, a putative S1 pocket and conserved candidate catalytic residues Thr1, Asp17 and Lys32(33). Nevertheless, we did not detect any YbAnbu peptidase or amidase activity. However, we could document orthophosphate production from ATP catalyzed by the ATP-grasp protein encoded in the Y. bercovieri Anbu operon.
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119
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Leloup N, Lössl P, Meijer DH, Brennich M, Heck AJR, Thies-Weesie DME, Janssen BJC. Low pH-induced conformational change and dimerization of sortilin triggers endocytosed ligand release. Nat Commun 2017; 8:1708. [PMID: 29167428 PMCID: PMC5700061 DOI: 10.1038/s41467-017-01485-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 09/19/2017] [Indexed: 11/24/2022] Open
Abstract
Low pH-induced ligand release and receptor recycling are important steps for endocytosis. The transmembrane protein sortilin, a β-propeller containing endocytosis receptor, internalizes a diverse set of ligands with roles in cell differentiation and homeostasis. The molecular mechanisms of pH-mediated ligand release and sortilin recycling are unresolved. Here we present crystal structures that show the sortilin luminal segment (s-sortilin) undergoes a conformational change and dimerizes at low pH. The conformational change, within all three sortilin luminal domains, provides an altered surface and the dimers sterically shield a large interface while bringing the two s-sortilin C-termini into close proximity. Biophysical and cell-based assays show that members of two different ligand families, (pro)neurotrophins and neurotensin, preferentially bind the sortilin monomer. This indicates that sortilin dimerization and conformational change discharges ligands and triggers recycling. More generally, this work may reveal a double mechanism for low pH-induced ligand release by endocytosis receptors. Sortilin is an endocytosis receptor with a luminal β-propeller domain. Here the authors present the structures of the β-propeller domain at neutral and acidic pH, which reveal that sortilin dimerises and undergoes conformational changes at low pH and further propose a model for low pH-induced ligand release by endocytosis receptors.
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Affiliation(s)
- Nadia Leloup
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Philip Lössl
- Biomolecular Mass Spectrometry & Proteomics and Netherlands Proteomics Center, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Dimphna H Meijer
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Martha Brennich
- European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, 38000, France
| | - Albert J R Heck
- Biomolecular Mass Spectrometry & Proteomics and Netherlands Proteomics Center, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Dominique M E Thies-Weesie
- Van't Hoff Laboratory for Physical and Colloid Chemistry, Debye Institute for Nanomaterials Science, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Bert J C Janssen
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands.
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120
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Yin Z, Machius M, Nestler EJ, Rudenko G. Activator Protein-1: redox switch controlling structure and DNA-binding. Nucleic Acids Res 2017; 45:11425-11436. [PMID: 28981703 PMCID: PMC5737521 DOI: 10.1093/nar/gkx795] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 08/31/2017] [Indexed: 01/07/2023] Open
Abstract
The transcription factor, activator protein-1 (AP-1), binds to cognate DNA under redox control; yet, the underlying mechanism has remained enigmatic. A series of crystal structures of the AP-1 FosB/JunD bZIP domains reveal ordered DNA-binding regions in both FosB and JunD even in absence DNA. However, while JunD is competent to bind DNA, the FosB bZIP domain must undergo a large conformational rearrangement that is controlled by a 'redox switch' centered on an inter-molecular disulfide bond. Solution studies confirm that FosB/JunD cannot undergo structural transition and bind DNA when the redox-switch is in the 'OFF' state, and show that the mid-point redox potential of the redox switch affords it sensitivity to cellular redox homeostasis. The molecular and structural studies presented here thus reveal the mechanism underlying redox-regulation of AP-1 Fos/Jun transcription factors and provide structural insight for therapeutic interventions targeting AP-1 proteins.
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Affiliation(s)
- Zhou Yin
- Department of Pharmacology and Toxicology, and the Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Mischa Machius
- Department of Pharmacology and Toxicology, and the Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Eric J. Nestler
- Fishberg Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L Levy Place, New York, NY 10029, USA
| | - Gabby Rudenko
- Department of Pharmacology and Toxicology, and the Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555, USA,To whom correspondence should be addressed. Tel: +1 409 772 6292; Fax: +1 409 772 9642;
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121
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Deyaert E, Wauters L, Guaitoli G, Konijnenberg A, Leemans M, Terheyden S, Petrovic A, Gallardo R, Nederveen-Schippers LM, Athanasopoulos PS, Pots H, Van Haastert PJM, Sobott F, Gloeckner CJ, Efremov R, Kortholt A, Versées W. A homologue of the Parkinson's disease-associated protein LRRK2 undergoes a monomer-dimer transition during GTP turnover. Nat Commun 2017; 8:1008. [PMID: 29044096 PMCID: PMC5714945 DOI: 10.1038/s41467-017-01103-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 08/18/2017] [Indexed: 11/24/2022] Open
Abstract
Mutations in LRRK2 are a common cause of genetic Parkinson's disease (PD). LRRK2 is a multi-domain Roco protein, harbouring kinase and GTPase activity. In analogy with a bacterial homologue, LRRK2 was proposed to act as a GTPase activated by dimerization (GAD), while recent reports suggest LRRK2 to exist under a monomeric and dimeric form in vivo. It is however unknown how LRRK2 oligomerization is regulated. Here, we show that oligomerization of a homologous bacterial Roco protein depends on the nucleotide load. The protein is mainly dimeric in the nucleotide-free and GDP-bound states, while it forms monomers upon GTP binding, leading to a monomer-dimer cycle during GTP hydrolysis. An analogue of a PD-associated mutation stabilizes the dimer and decreases the GTPase activity. This work thus provides insights into the conformational cycle of Roco proteins and suggests a link between oligomerization and disease-associated mutations in LRRK2.
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Affiliation(s)
- Egon Deyaert
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Lina Wauters
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Department of Cell Biochemistry, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Giambattista Guaitoli
- German Center for Neurodegenerative Diseases (DZNE), 72076, Tübingen, Germany
- Eberhard Karls University, Institute for Ophthalmic Research, Center for Ophthalmology, 72076, Tübingen, Germany
| | - Albert Konijnenberg
- Department of Chemistry, Biomolecular & Analytical Mass Spectrometry group, University of Antwerp, 2020, Antwerp, Belgium
| | - Margaux Leemans
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Susanne Terheyden
- Department of Cell Biochemistry, University of Groningen, Groningen, 9747 AG, The Netherlands
- Structural Biology Group, Max-Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Arsen Petrovic
- Department of Mechanistic Cell Biology, Max-Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Rodrigo Gallardo
- VIB Center for Brain & Disease Research, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, PB 802, 3000, Leuven, Belgium
| | | | | | - Henderikus Pots
- Department of Cell Biochemistry, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Peter J M Van Haastert
- Department of Cell Biochemistry, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Frank Sobott
- Department of Chemistry, Biomolecular & Analytical Mass Spectrometry group, University of Antwerp, 2020, Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, Leeds, UK
- School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, Leeds, UK
| | - Christian Johannes Gloeckner
- German Center for Neurodegenerative Diseases (DZNE), 72076, Tübingen, Germany
- Eberhard Karls University, Institute for Ophthalmic Research, Center for Ophthalmology, 72076, Tübingen, Germany
| | - Rouslan Efremov
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Arjan Kortholt
- Department of Cell Biochemistry, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Wim Versées
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium.
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
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122
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Aik WS, Lin MH, Tan D, Tripathy A, Marzluff WF, Dominski Z, Chou CY, Tong L. The N-terminal domains of FLASH and Lsm11 form a 2:1 heterotrimer for histone pre-mRNA 3'-end processing. PLoS One 2017; 12:e0186034. [PMID: 29020104 PMCID: PMC5636114 DOI: 10.1371/journal.pone.0186034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 09/23/2017] [Indexed: 11/18/2022] Open
Abstract
Unlike canonical pre-mRNAs, animal replication-dependent histone pre-mRNAs lack introns and are processed at the 3'-end by a mechanism distinct from cleavage and polyadenylation. They have a 3' stem loop and histone downstream element (HDE) that are recognized by stem-loop binding protein (SLBP) and U7 snRNP, respectively. The N-terminal domain (NTD) of Lsm11, a component of U7 snRNP, interacts with FLASH NTD and these two proteins recruit the histone cleavage complex containing the CPSF-73 endonuclease for the cleavage reaction. Here, we determined crystal structures of FLASH NTD and found that it forms a coiled-coil dimer. Using solution light scattering, we characterized the stoichiometry of the FLASH NTD-Lsm11 NTD complex and found that it is a 2:1 heterotrimer, which is supported by observations from analytical ultracentrifugation and crosslinking.
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Affiliation(s)
- Wei Shen Aik
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Min-Han Lin
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Dazhi Tan
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Ashutosh Tripathy
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - William F. Marzluff
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Zbigniew Dominski
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Chi-Yuan Chou
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
- * E-mail:
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Xiao H, Wang F, Wisniewski J, Shaytan AK, Ghirlando R, FitzGerald PC, Huang Y, Wei D, Li S, Landsman D, Panchenko AR, Wu C. Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres. Genes Dev 2017; 31:1958-1972. [PMID: 29074736 PMCID: PMC5710141 DOI: 10.1101/gad.304782.117] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/05/2017] [Indexed: 12/16/2022]
Abstract
Histone CENP-A-containing nucleosomes play an important role in nucleating kinetochores at centromeres for chromosome segregation. However, the molecular mechanisms by which CENP-A nucleosomes engage with kinetochore proteins are not well understood. Here, we report the finding of a new function for the budding yeast Cse4/CENP-A histone-fold domain interacting with inner kinetochore protein Mif2/CENP-C. Strikingly, we also discovered that AT-rich centromere DNA has an important role for Mif2 recruitment. Mif2 contacts one side of the nucleosome dyad, engaging with both Cse4 residues and AT-rich nucleosomal DNA. Both interactions are directed by a contiguous DNA- and histone-binding domain (DHBD) harboring the conserved CENP-C motif, an AT hook, and RK clusters (clusters enriched for arginine-lysine residues). Human CENP-C has two related DHBDs that bind preferentially to DNA sequences of higher AT content. Our findings suggest that a DNA composition-based mechanism together with residues characteristic for the CENP-A histone variant contribute to the specification of centromere identity.
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Affiliation(s)
- Hua Xiao
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Feng Wang
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jan Wisniewski
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Alexey K Shaytan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Peter C FitzGerald
- Genome Analysis Unit, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Yingzi Huang
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Debbie Wei
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Shipeng Li
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - David Landsman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Anna R Panchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Carl Wu
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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124
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Chen B, Chou HT, Brautigam CA, Xing W, Yang S, Henry L, Doolittle LK, Walz T, Rosen MK. Rac1 GTPase activates the WAVE regulatory complex through two distinct binding sites. eLife 2017; 6. [PMID: 28949297 PMCID: PMC5614565 DOI: 10.7554/elife.29795] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/01/2017] [Indexed: 01/01/2023] Open
Abstract
The Rho GTPase Rac1 activates the WAVE regulatory complex (WRC) to drive Arp2/3 complex-mediated actin polymerization, which underpins diverse cellular processes. Here we report the structure of a WRC-Rac1 complex determined by cryo-electron microscopy. Surprisingly, Rac1 is not located at the binding site on the Sra1 subunit of the WRC previously identified by mutagenesis and biochemical data. Rather, it binds to a distinct, conserved site on the opposite end of Sra1. Biophysical and biochemical data on WRC mutants confirm that Rac1 binds to both sites, with the newly identified site having higher affinity and both sites required for WRC activation. Our data reveal that the WRC is activated by simultaneous engagement of two Rac1 molecules, suggesting a mechanism by which cells may sense the density of active Rac1 at membranes to precisely control actin assembly. Our cells contain a network of filaments made up of a protein called actin. Just like the skeleton that supports our body, the actin ‘cytoskeleton’ gives a cell its shape and strength. Actin filaments are also critical for many other processes including enabling cells to move and divide. The assembly of actin filaments must be properly controlled so that they are formed at the right time and place within the cell. A complex of proteins known as the WAVE Regulatory Complex (WRC) promotes the assembly of actin filaments. The complex contains a region called the VCA, which is able to bind to and activate another protein to make the new actin filaments. The WRC regulates filament assembly by controlling the availability of the VCA in a way that is similar to opening and closing a safe box. When new actin filaments are not needed, the safe box is closed and the VCA is not available. However, when cells need to make new actin filaments, the WRC is opened to release the VCA region so that it is able to bind to the filament-producing protein. Previous studies have shown that a protein called Rac1 acts as a key to open the WRC and trigger actin filament assembly. But it remains unclear how this works. A major obstacle to studying this process is that Rac1 and the WRC only weakly interact with each other, which makes it difficult to capture the interaction under experimental conditions. To overcome this obstacle, Chen et al. tethered a Rac1 molecule to the WRC in order to make the interaction more stable. A technique called cryo-electron microscopy was used to study the three-dimensional shape of this Rac1-WRC complex. Unexpectedly, Rac1 was attached to a different part of the WRC than the site predicted by previous studies. Further experiments showed that Rac1 needs to bind to both of these sites at the same time in order to open the WRC and release VCA, similar to using two keys to open one safe box for increased security. Some cancers, neurological disorders and other diseases can be caused by defects in WRC and Rac1 activity. Therefore, these findings could lead to new ways to treat these conditions in human patients.
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Affiliation(s)
- Baoyu Chen
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, United States
| | - Hui-Ting Chou
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Chad A Brautigam
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, United States.,Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Wenmin Xing
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, United States
| | - Sheng Yang
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, United States
| | - Lisa Henry
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, United States
| | - Lynda K Doolittle
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, United States
| | - Thomas Walz
- Rockefeller University, New York, United States
| | - Michael K Rosen
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, United States
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125
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Rimmerman D, Leshchev D, Hsu DJ, Hong J, Kosheleva I, Chen LX. Direct Observation of Insulin Association Dynamics with Time-Resolved X-ray Scattering. J Phys Chem Lett 2017; 8:4413-4418. [PMID: 28853898 PMCID: PMC5804350 DOI: 10.1021/acs.jpclett.7b01720] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Biological functions frequently require protein-protein interactions that involve secondary and tertiary structural perturbation. Here we study protein-protein dissociation and reassociation dynamics in insulin, a model system for protein oligomerization. Insulin dimer dissociation into monomers was induced by a nanosecond temperature-jump (T-jump) of ∼8 °C in aqueous solution, and the resulting protein and solvent dynamics were tracked by time-resolved X-ray solution scattering (TRXSS) on time scales of 10 ns to 100 ms. The protein scattering signals revealed the formation of five distinguishable transient species during the association process that deviate from simple two-state kinetics. Our results show that the combination of T-jump pump coupled to TRXSS probe allows for direct tracking of structural dynamics in nonphotoactive proteins.
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Affiliation(s)
- Dolev Rimmerman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Denis Leshchev
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Darren J. Hsu
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Jiyun Hong
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, United States
| | - Lin X. Chen
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
- Corresponding Author, ,
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126
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Chaturvedi SK, Ma J, Zhao H, Schuck P. Use of fluorescence-detected sedimentation velocity to study high-affinity protein interactions. Nat Protoc 2017; 12:1777-1791. [PMID: 28771239 PMCID: PMC7466938 DOI: 10.1038/nprot.2017.064] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Sedimentation velocity (SV) analytical ultracentrifugation (AUC) is a classic technique for the real-time observation of free macromolecular migration in solution driven by centrifugal force. This enables the analysis of macromolecular mass, shape, size distribution, and interactions. Although traditionally limited to determination of the sedimentation coefficient and binding affinity of proteins in the micromolar range, the implementation of modern detection and data analysis techniques has resulted in marked improvements in detection sensitivity and size resolution during the past decades. Fluorescence optical detection now permits the detection of recombinant proteins with fluorescence excitation at 488 or 561 nm at low picomolar concentrations, allowing for the study of high-affinity protein self-association and hetero-association. Compared with other popular techniques for measuring high-affinity protein-protein interactions, such as biosensing or calorimetry, the high size resolution of complexes at picomolar concentrations obtained with SV offers a distinct advantage in sensitivity and flexibility of the application. Here, we present a basic protocol for carrying out fluorescence-detected SV experiments and the determination of the size distribution and affinity of protein-antibody complexes with picomolar KD values. Using an EGFP-nanobody interaction as a model, this protocol describes sample preparation, ultracentrifugation, data acquisition, and data analysis. A variation of the protocol applying traditional absorbance or an interference optical system can be used for protein-protein interactions in the micromolar KD value range. Sedimentation experiments typically take ∼3 h of preparation and 6-12 h of run time, followed by data analysis (typically taking 1-3 h).
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Affiliation(s)
- Sumit K. Chaturvedi
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Jia Ma
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, U.S.A
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127
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Jančaříková G, Houser J, Dobeš P, Demo G, Hyršl P, Wimmerová M. Characterization of novel bangle lectin from Photorhabdus asymbiotica with dual sugar-binding specificity and its effect on host immunity. PLoS Pathog 2017; 13:e1006564. [PMID: 28806750 PMCID: PMC5584973 DOI: 10.1371/journal.ppat.1006564] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 09/05/2017] [Accepted: 07/31/2017] [Indexed: 01/08/2023] Open
Abstract
Photorhabdus asymbiotica is one of the three recognized species of the Photorhabdus genus, which consists of gram-negative bioluminescent bacteria belonging to the family Morganellaceae. These bacteria live in a symbiotic relationship with nematodes from the genus Heterorhabditis, together forming a complex that is highly pathogenic for insects. Unlike other Photorhabdus species, which are strictly entomopathogenic, P. asymbiotica is unique in its ability to act as an emerging human pathogen. Analysis of the P. asymbiotica genome identified a novel fucose-binding lectin designated PHL with a strong sequence similarity to the recently described P. luminescens lectin PLL. Recombinant PHL exhibited high affinity for fucosylated carbohydrates and the unusual disaccharide 3,6-O-Me2-Glcβ1-4(2,3-O-Me2)Rhaα-O-(p-C6H4)-OCH2CH2NH2 from Mycobacterium leprae. Based on its crystal structure, PHL forms a seven-bladed β-propeller assembling into a homo-dimer with an inter-subunit disulfide bridge. Investigating complexes with different ligands revealed the existence of two sets of binding sites per monomer-the first type prefers l-fucose and its derivatives, whereas the second type can bind d-galactose. Based on the sequence analysis, PHL could contain up to twelve binding sites per monomer. PHL was shown to interact with all types of red blood cells and insect haemocytes. Interestingly, PHL inhibited the production of reactive oxygen species induced by zymosan A in human blood and antimicrobial activity both in human blood, serum and insect haemolymph. Concurrently, PHL increased the constitutive level of oxidants in the blood and induced melanisation in haemolymph. Our results suggest that PHL might play a crucial role in the interaction of P. asymbiotica with both human and insect hosts.
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Affiliation(s)
- Gita Jančaříková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Josef Houser
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Pavel Dobeš
- Department of Animal Physiology and Immunology, Institute of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Gabriel Demo
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Pavel Hyršl
- Department of Animal Physiology and Immunology, Institute of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Michaela Wimmerová
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
- * E-mail:
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128
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Bláha J, Kalousková B, Skořepa O, Pažický S, Novák P, Vaněk O. High-level expression and purification of soluble form of human natural killer cell receptor NKR-P1 in HEK293S GnTI - cells. Protein Expr Purif 2017; 140:36-43. [PMID: 28757467 DOI: 10.1016/j.pep.2017.07.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 02/09/2023]
Abstract
Human natural killer receptor protein 1 (NKR-P1, CD161, gene klrb1) is a C-type lectin-like receptor of natural killer (NK) cells responsible for recognition of its cognate protein ligand lectin-like transcript 1 (LLT1). NKR-P1 is the single human orthologue of the prototypical rodent NKR-P1 receptors. Naturally, human NKR-P1 is expressed on the surface of NK cells, where it serves as inhibitory receptor; and on T and NKT cells functioning as co-stimulatory receptor promoting secretion of IFNγ. Most notably, it is expressed on Th17 and Tc17 lymphocytes where presumably promotes targeting into LLT1 expressing immunologically privileged niches. We tested effect of different protein tags (SUMO, TRX, GST, MsyB) on expression of soluble NKR-P1 in E. coli. Then we optimized the expression construct of soluble NKR-P1 by preparing a library of expression constructs in pOPING vector containing the extracellular lectin-like domain with different length of the putative N-terminal stalk region and tested its expression in Sf9 and HEK293 cells. Finally, a high-level expression of soluble NKR-P1 was achieved by stable expression in suspension-adapted HEK293S GnTI- cells utilizing pOPINGTTneo expression vector. Purified soluble NKR-P1 is homogeneous, deglycosylatable, crystallizable and monomeric in solution, as shown by size-exclusion chromatography, multi-angle light scattering and analytical ultracentrifugation.
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Affiliation(s)
- Jan Bláha
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic
| | - Barbora Kalousková
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic
| | - Ondřej Skořepa
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic
| | - Samuel Pažický
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic
| | - Petr Novák
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic; Institute of Microbiology, The Czech Academy of Sciences, BIOCEV, Průmyslová 595, 25250 Vestec, Czech Republic
| | - Ondřej Vaněk
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic.
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129
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Wei G, Su Z, Reynolds NP, Arosio P, Hamley IW, Gazit E, Mezzenga R. Self-assembling peptide and protein amyloids: from structure to tailored function in nanotechnology. Chem Soc Rev 2017; 46:4661-4708. [PMID: 28530745 PMCID: PMC6364806 DOI: 10.1039/c6cs00542j] [Citation(s) in RCA: 529] [Impact Index Per Article: 75.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Self-assembled peptide and protein amyloid nanostructures have traditionally been considered only as pathological aggregates implicated in human neurodegenerative diseases. In more recent times, these nanostructures have found interesting applications as advanced materials in biomedicine, tissue engineering, renewable energy, environmental science, nanotechnology and material science, to name only a few fields. In all these applications, the final function depends on: (i) the specific mechanisms of protein aggregation, (ii) the hierarchical structure of the protein and peptide amyloids from the atomistic to mesoscopic length scales and (iii) the physical properties of the amyloids in the context of their surrounding environment (biological or artificial). In this review, we will discuss recent progress made in the field of functional and artificial amyloids and highlight connections between protein/peptide folding, unfolding and aggregation mechanisms, with the resulting amyloid structure and functionality. We also highlight current advances in the design and synthesis of amyloid-based biological and functional materials and identify new potential fields in which amyloid-based structures promise new breakthroughs.
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Affiliation(s)
- Gang Wei
- Faculty of Production Engineering, University of Bremen, Bremen,
Germany
| | - Zhiqiang Su
- State Key Laboratory of Chemical Resource Engineering, Beijing
University of Chemical Technology, China
| | - Nicholas P. Reynolds
- ARC Training Centre for Biodevices, Swinburne University of
Technology, Melbourne, Australia
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, ETH-Zurich,
Switzerland
| | | | - Ehud Gazit
- Faculty of Life Sciences, Tel Aviv University, Israel
| | - Raffaele Mezzenga
- Department of Health Science and Technology, ETH-Zurich,
Switzerland
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130
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Nawata M, Tsutsumi H, Kobayashi Y, Unzai S, Mine S, Nakamura T, Uegaki K, Kamikubo H, Kataoka M, Hamada D. Heat-induced native dimerization prevents amyloid formation by variable domain from immunoglobulin light-chain REI. FEBS J 2017; 284:3114-3127. [PMID: 28736891 DOI: 10.1111/febs.14181] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 06/15/2017] [Accepted: 07/19/2017] [Indexed: 11/29/2022]
Abstract
Amyloid light-chain (AL) amyloidosis is a protein-misfolding disease characterized by accumulation of immunoglobulin light chains (LCs) into amyloid fibrils. Dimerization of a full length or variable domain (VL ) of LC serves to stabilize the native state and prevent the formation of amyloid fibrils. We here analyzed the thermodynamic properties of dimerization and unfolding reactions by nonamyloidogenic VL from REI LC or its monomeric Y96K mutant using sedimentation velocity and circular dichroism. The data indicate that the equilibrium shifts to native dimerization for wild-type REI VL by elevating temperature due to the negative enthalpy change for dimer dissociation (-81.2 kJ·mol-1 ). The Y96K mutation did not affect the stability of the monomeric native state but increased amyloidogenicity. These results suggest that the heat-induced native homodimerization is the major factor preventing amyloid formation by wild-type REI VL . Heat-induced native oligomerization may be an efficient strategy to avoid the formation of misfolded aggregates particularly for thermostable proteins that are used at elevated temperatures under conditions where other proteins tend to misfold. DATABASE Structural data are available in the Protein Data Bank under the accession numbers 5XP1 and 5XQY.
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Affiliation(s)
| | | | | | - Satoru Unzai
- Protein Design Laboratory, Yokohama City University, Japan
| | - Shouhei Mine
- National Institute of Advanced Industrial Science and Technology (AIST), Ikeda, Japan
| | - Tsutomu Nakamura
- National Institute of Advanced Industrial Science and Technology (AIST), Ikeda, Japan
| | - Koichi Uegaki
- National Institute of Advanced Industrial Science and Technology (AIST), Ikeda, Japan
| | - Hironari Kamikubo
- Laboratory of Bioenergetics and Biophysics, Nara Institute of Science and Technology (NAIST), Ikoma, Japan
| | - Mikio Kataoka
- Laboratory of Bioenergetics and Biophysics, Nara Institute of Science and Technology (NAIST), Ikoma, Japan
| | - Daizo Hamada
- Graduate School of Medicine, Kobe University, Japan.,Department of Life Sciences, Graduate School of Bioresources, Mie University, Tsu, Japan.,Graduate School of Engineering, Kobe University, Japan.,Center for Applied Structural Science (CASS), Kobe University, Japan
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131
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Jing X, Evangelista Falcon W, Baudry J, Serpersu EH. Thermophilic Enzyme or Mesophilic Enzyme with Enhanced Thermostability: Can We Draw a Line? J Phys Chem B 2017; 121:7086-7094. [DOI: 10.1021/acs.jpcb.7b04519] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Wilfredo Evangelista Falcon
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Jerome Baudry
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
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132
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Larson AG, Elnatan D, Keenen MM, Trnka MJ, Johnston JB, Burlingame AL, Agard DA, Redding S, Narlikar GJ. Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin. Nature 2017; 547:236-240. [PMID: 28636604 PMCID: PMC5606208 DOI: 10.1038/nature22822] [Citation(s) in RCA: 1099] [Impact Index Per Article: 157.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 05/16/2017] [Indexed: 01/15/2023]
Abstract
Gene silencing by heterochromatin is proposed to occur in part as a result of the ability of heterochromatin protein 1 (HP1) proteins to spread across large regions of the genome, compact the underlying chromatin and recruit diverse ligands. Here we identify a new property of the human HP1α protein: the ability to form phase-separated droplets. While unmodified HP1α is soluble, either phosphorylation of its N-terminal extension or DNA binding promotes the formation of phase-separated droplets. Phosphorylation-driven phase separation can be promoted or reversed by specific HP1α ligands. Known components of heterochromatin such as nucleosomes and DNA preferentially partition into the HP1α droplets, but molecules such as the transcription factor TFIIB show no preference. Using a single-molecule DNA curtain assay, we find that both unmodified and phosphorylated HP1α induce rapid compaction of DNA strands into puncta, although with different characteristics. We show by direct protein delivery into mammalian cells that an HP1α mutant incapable of phase separation in vitro forms smaller and fewer nuclear puncta than phosphorylated HP1α. These findings suggest that heterochromatin-mediated gene silencing may occur in part through sequestration of compacted chromatin in phase-separated HP1 droplets, which are dissolved or formed by specific ligands on the basis of nuclear context.
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Affiliation(s)
- Adam G. Larson
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Daniel Elnatan
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Madeline M. Keenen
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael J. Trnka
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jonathan B. Johnston
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alma L. Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - David A. Agard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sy Redding
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Geeta J. Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
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133
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Krajewska J, Modrak-Wójcik A, Arent ZJ, Więckowski D, Zolkiewski M, Bzowska A, Kędzierska-Mieszkowska S. Characterization of the molecular chaperone ClpB from the pathogenic spirochaete Leptospira interrogans. PLoS One 2017; 12:e0181118. [PMID: 28700685 PMCID: PMC5507356 DOI: 10.1371/journal.pone.0181118] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/26/2017] [Indexed: 11/18/2022] Open
Abstract
Leptospira interrogans is a spirochaete responsible for leptospirosis in mammals. The molecular mechanisms of the Leptospira virulence remain mostly unknown. Recently, it has been demonstrated that an AAA+ chaperone ClpB (a member of the Hsp100 family) from L. interrogans (ClpBLi) is not only essential for survival of Leptospira under the thermal and oxidative stresses, but also during infection of a host. The aim of this study was to provide further insight into the role of ClpB in the pathogenic spirochaetes and explore its biochemical properties. We found that a non-hydrolysable ATP analogue, ATPγS, but not AMP-PNP induces the formation of ClpBLi hexamers and stabilizes the associated form of the chaperone. ADP also induces structural changes in ClpBLi and promotes its self-assembly, but does not produce full association into the hexamers. We also demonstrated that ClpBLi exhibits a weak ATPase activity that is stimulated by κ-casein and poly-lysine, and may mediate protein disaggregation independently from the DnaK chaperone system. Unexpectedly, the presence of E. coli DnaK/DnaJ/GrpE did not significantly affect the disaggregation activity of ClpBLi and ClpBLi did not substitute for the ClpBEc function in the clpB-null E. coli strain. This result underscores the species-specificity of the ClpB cooperation with the co-chaperones and is most likely due to a loss of interactions between the ClpBLi middle domain and the E. coli DnaK. We also found that ClpBLi interacts more efficiently with the aggregated G6PDH in the presence of ATPγS rather than ATP. Our results indicate that ClpB's importance during infection might be due to its role as a molecular chaperone involved in reactivation of protein aggregates.
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Affiliation(s)
- Joanna Krajewska
- Department of General and Medical Biochemistry, University of Gdańsk, Faculty of Biology, Gdańsk, Poland
| | - Anna Modrak-Wójcik
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Zbigniew J. Arent
- University Centre of Veterinary Medicine UJ-UR, University of Agriculture in Krakow, Krakow, Poland
| | - Daniel Więckowski
- Department of General and Medical Biochemistry, University of Gdańsk, Faculty of Biology, Gdańsk, Poland
| | - Michal Zolkiewski
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, United States of America
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
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134
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Preis W, Bestehorn A, Buchner J, Haslbeck M. An alternative splice variant of human αA-crystallin modulates the oligomer ensemble and the chaperone activity of α-crystallins. Cell Stress Chaperones 2017; 22:541-552. [PMID: 28214988 PMCID: PMC5465031 DOI: 10.1007/s12192-017-0772-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/31/2017] [Accepted: 02/01/2017] [Indexed: 01/26/2023] Open
Abstract
In humans, ten genes encode small heat shock proteins with lens αA-crystallin and αB-crystallin representing two of the most prominent members. The canonical isoforms of αA-crystallin and αB-crystallin collaborate in the eye lens to prevent irreversible protein aggregation and preserve visual acuity. α-Crystallins form large polydisperse homo-oligomers and hetero-oligomers and as part of the proteostasis system bind substrate proteins in non-native conformations, thereby stabilizing them. Here, we analyzed a previously uncharacterized, alternative splice variant (isoform 2) of human αA-crystallin with an exchanged N-terminal sequence. This variant shows the characteristic α-crystallin secondary structure, exists on its own predominantly in a monomer-dimer equilibrium, and displays only low chaperone activity. However, the variant is able to integrate into higher order oligomers of canonical αA-crystallin and αB-crystallin as well as their hetero-oligomer. The presence of the variant leads to the formation of new types of higher order hetero-oligomers with an overall decreased number of subunits and enhanced chaperone activity. Thus, alternative mRNA splicing of human αA-crystallin leads to an additional, formerly not characterized αA-crystallin species which is able to modulate the properties of the canonical ensemble of α-crystallin oligomers.
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Affiliation(s)
- Waldemar Preis
- Department Chemie, Center for Integrated Protein Science, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Annika Bestehorn
- Department Chemie, Center for Integrated Protein Science, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Johannes Buchner
- Department Chemie, Center for Integrated Protein Science, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Martin Haslbeck
- Department Chemie, Center for Integrated Protein Science, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany.
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135
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Sagar V, Chaturvedi SK, Schuck P, Wistow G. Crystal Structure of Chicken γS-Crystallin Reveals Lattice Contacts with Implications for Function in the Lens and the Evolution of the βγ-Crystallins. Structure 2017. [PMID: 28648607 PMCID: PMC5518705 DOI: 10.1016/j.str.2017.05.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Previous attempts to crystallize mammalian γS-crystallin were unsuccessful. Native L16 chicken γS crystallized avidly while the Q16 mutant did not. The x-ray structure for chicken γS at 2.3Å resolution shows the canonical structure of the superfamily plus a well-ordered N-arm aligned with a β-sheet of a neighboring N-domain. L16 is also in a lattice contact, partially shielded from solvent. Unexpectedly, the major lattice contact matches a conserved interface (QR) in the multimeric β-crystallins. QR shows little conservation of residue contacts, except for one between symmetry-related tyrosines, but molecular dipoles for the proteins with QR show striking similarities while other γ-crystallins differ. In γS, QR has few hydrophobic contacts and features a thin layer of tightly bound water. The free energy of QR is slightly repulsive and AUC confirms no dimerization in solution. The lattice contacts suggest how γcrystallins allow close packing without aggregation in the crowded environment of the lens.
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Affiliation(s)
- Vatsala Sagar
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Building 6, Room 106, Bethesda, MD 20892, USA
| | - Sumit K Chaturvedi
- Dynamics of Macromolecular Assembly Section, LCIMB, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, LCIMB, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Graeme Wistow
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Building 6, Room 106, Bethesda, MD 20892, USA.
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136
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Minici C, Gounari M, Übelhart R, Scarfò L, Dühren-von Minden M, Schneider D, Tasdogan A, Alkhatib A, Agathangelidis A, Ntoufa S, Chiorazzi N, Jumaa H, Stamatopoulos K, Ghia P, Degano M. Distinct homotypic B-cell receptor interactions shape the outcome of chronic lymphocytic leukaemia. Nat Commun 2017; 8:15746. [PMID: 28598442 PMCID: PMC5472768 DOI: 10.1038/ncomms15746] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 04/25/2017] [Indexed: 01/04/2023] Open
Abstract
Cell-autonomous B-cell receptor (BcR)-mediated signalling is a hallmark feature of the neoplastic B lymphocytes in chronic lymphocytic leukaemia (CLL). Here we elucidate the structural basis of autonomous activation of CLL B cells, showing that BcR immunoglobulins initiate intracellular signalling through homotypic interactions between epitopes that are specific for each subgroup of patients with homogeneous clinicobiological profiles. The molecular details of the BcR–BcR interactions apparently dictate the clinical course of disease, with stronger affinities and longer half-lives in indolent cases, and weaker, short-lived contacts mediating the aggressive ones. The diversity of homotypic BcR contacts leading to cell-autonomous signalling reconciles the existence of a shared pathogenic mechanism with the biological and clinical heterogeneity of CLL and offers opportunities for innovative treatment strategies. Chronic lymphocytic leukaemia (CLL) is characterized by cell-autonomous B-cell receptor (BcR)-mediated signalling of neoplastic B lymphocytes. Here the authors unveil the structural basis and diversity of activatory homotypic BcR contacts and link them with CLL heterogeneity and the clinical outcome.
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Affiliation(s)
- Claudia Minici
- Biocrystallography Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, via Olgettina 58, 20132 Milan, Italy.,Università Vita-Salute San Raffaele, 20132 Milan, Italy
| | - Maria Gounari
- B-cell Neoplasia Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | | | - Lydia Scarfò
- Università Vita-Salute San Raffaele, 20132 Milan, Italy.,B-cell Neoplasia Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy.,Strategic Research Program on CLL, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | | | - Dunja Schneider
- Centre for Biological Signaling Studies, Faculty of Biology, Albert-Ludwigs University of Freiburg, 79104 Freiburg, Germany
| | | | - Alabbas Alkhatib
- Centre for Biological Signaling Studies, Faculty of Biology, Albert-Ludwigs University of Freiburg, 79104 Freiburg, Germany
| | - Andreas Agathangelidis
- B-cell Neoplasia Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Stavroula Ntoufa
- Institute of Applied Biosciences, Center for Research and Technology, 57001 Thessaloniki, Greece
| | - Nicholas Chiorazzi
- The Feinstein Institute for Medical Research, Manhasset, New York 11030, USA
| | | | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Center for Research and Technology, 57001 Thessaloniki, Greece.,Department of Immunology, Genetics and Pathology, Uppsala University, 75105 Uppsala, Sweden
| | - Paolo Ghia
- Università Vita-Salute San Raffaele, 20132 Milan, Italy.,B-cell Neoplasia Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy.,Strategic Research Program on CLL, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Massimo Degano
- Biocrystallography Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, via Olgettina 58, 20132 Milan, Italy
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137
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Rodríguez Nassif A, de la Arada I, Arrondo JL, Pastrana-Rios B. 2D IR Correlation Spectroscopy in the Determination of Aggregation and Stability of KH Domain GXXG Loop Peptide in the Presence and Absence of Trifluoroacetate. Anal Chem 2017; 89:5765-5775. [PMID: 28459550 DOI: 10.1021/acs.analchem.6b04800] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Trifluoroacetate (TFA) is a strong anion byproduct of solid-phase peptide synthesis. Fourier transform infrared (FT-IR) spectroscopy can be used to ascertain the presence of this excipient in peptide samples for quality assessment. TFA absorbs as a strong sharp peak (1675 cm-1) within the amide I' band of the spectral region. A peptide sample and the TFA excipient can be studied simultaneously by FT-IR and 2D IR correlation spectroscopies. In addition, these techniques are able to determine the effect of TFA on the stability of the peptide. Herein, we describe the spectroscopic characterization of the GXXG loop peptide (GXXGlp), which is present in KH domain containing proteins. The sequence of the Homo sapiens Krr1 GXXGlp is evolutionarily conserved (165KRRQRLIGPKGSTLKALELLTNCY189) and has been associated with ssDNA interaction and ribosome biogenesis. Our goal was to determine the structural elements present in this peptide and evaluate whether TFA affects the stability of GXXGlp during thermal stress. We observed differences in the molecular behavior of the synthetic peptide in the presence and absence of TFA at various peptide concentrations. Finally, 2D IR correlation spectroscopy was used for the determination of the unfolding process, mechanism and extent of peptide aggregation, and the effect of TFA on the stability of the peptide. This spectroscopic method can be applied to the characterization of any synthetic peptide.
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Affiliation(s)
- Aslin Rodríguez Nassif
- Department of Chemistry, University of Puerto Rico , Mayagüez Campus, Mayagüez, Puerto Rico 00681-9019, United States
| | - Igor de la Arada
- Biofisika Institute and Biochemistry and Molecular Biology Department, CSIC and University of Basque Country , Bilbao, 48080, Spain
| | - José Luis Arrondo
- Biofisika Institute and Biochemistry and Molecular Biology Department, CSIC and University of Basque Country , Bilbao, 48080, Spain
| | - Belinda Pastrana-Rios
- Department of Chemistry, University of Puerto Rico , Mayagüez Campus, Mayagüez, Puerto Rico 00681-9019, United States.,Protein Research Center, University of Puerto Rico , Mayagüez Campus, Mayagüez, Puerto Rico 00681-9019, United States
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138
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Purification of bacterial membrane sensor kinases and biophysical methods for determination of their ligand and inhibitor interactions. Biochem Soc Trans 2017; 44:810-23. [PMID: 27284046 PMCID: PMC4900758 DOI: 10.1042/bst20160023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Indexed: 01/20/2023]
Abstract
This article reviews current methods for the reliable heterologous overexpression in Escherichia coli and purification of milligram quantities of bacterial membrane sensor kinase (MSK) proteins belonging to the two-component signal transduction family of integral membrane proteins. Many of these methods were developed at Leeds alongside Professor Steve Baldwin to whom this review is dedicated. It also reviews two biophysical methods that we have adapted successfully for studies of purified MSKs and other membrane proteins–synchrotron radiation circular dichroism (SRCD) spectroscopy and analytical ultracentrifugation (AUC), both of which are non-immobilization and matrix-free methods that require no labelling strategies. Other techniques such as isothermal titration calorimetry (ITC) also share these features but generally require high concentrations of material. In common with many other biophysical techniques, both of these biophysical methods provide information regarding membrane protein conformation, oligomerization state and ligand binding, but they possess the additional advantage of providing direct assessments of whether ligand binding interactions are accompanied by conformational changes. Therefore, both methods provide a powerful means by which to identify and characterize inhibitor binding and any associated protein conformational changes, thereby contributing valuable information for future drug intervention strategies directed towards bacterial MSKs.
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139
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Probing the Roles of Calcium-Binding Sites during the Folding of Human Peptidylarginine Deiminase 4. Sci Rep 2017; 7:2429. [PMID: 28546558 PMCID: PMC5445078 DOI: 10.1038/s41598-017-02677-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 04/18/2017] [Indexed: 11/24/2022] Open
Abstract
Our recent studies of peptidylarginine deiminase 4 (PAD4) demonstrate that its non-catalytic Ca2+-binding sites play a crucial role in the assembly of the correct geometry of the enzyme. Here, we examined the folding mechanism of PAD4 and the role of Ca2+ ions in the folding pathway. Multiple mutations were introduced into the calcium-binding sites, and these mutants were termed the Ca1_site, Ca2_site, Ca3_site, Ca4_site and Ca5_site mutants. Our data indicate that during the unfolding process, the PAD4 dimer first dissociates into monomers, and the monomers then undergo a three-state denaturation process via an intermediate state formation. In addition, Ca2+ ions assist in stabilizing the folding intermediate, particularly through binding to the Ca3_site and Ca4_site to ensure the correct and active conformation of PAD4. The binding of calcium ions to the Ca1_site and Ca2_site is directly involved in the catalytic action of the enzyme. Finally, this study proposes a model for the folding of PAD4. The nascent polypeptide chains of PAD4 are first folded into monomeric intermediate states, then continue to fold into monomers, and ultimately assemble into a functional and dimeric PAD4 enzyme, and cellular Ca2+ ions may be the critical factor governing the interchange.
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140
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Chaturvedi SK, Zhao H, Schuck P. Sedimentation of Reversibly Interacting Macromolecules with Changes in Fluorescence Quantum Yield. Biophys J 2017; 112:1374-1382. [PMID: 28402880 DOI: 10.1016/j.bpj.2017.02.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/10/2017] [Accepted: 02/21/2017] [Indexed: 11/29/2022] Open
Abstract
Sedimentation velocity analytical ultracentrifugation with fluorescence detection has emerged as a powerful method for the study of interacting systems of macromolecules. It combines picomolar sensitivity with high hydrodynamic resolution, and can be carried out with photoswitchable fluorophores for multicomponent discrimination, to determine the stoichiometry, affinity, and shape of macromolecular complexes with dissociation equilibrium constants from picomolar to micromolar. A popular approach for data interpretation is the determination of the binding affinity by isotherms of weight-average sedimentation coefficients sw. A prevailing dogma in sedimentation analysis is that the weight-average sedimentation coefficient from the transport method corresponds to the signal- and population-weighted average of all species. We show that this does not always hold true for systems that exhibit significant signal changes with complex formation-properties that may be readily encountered in practice, e.g., from a change in fluorescence quantum yield. Coupled transport in the reaction boundary of rapidly reversible systems can make significant contributions to the observed migration in a way that cannot be accounted for in the standard population-based average. Effective particle theory provides a simple physical picture for the reaction-coupled migration process. On this basis, we develop a more general binding model that converges to the well-known form of sw with constant signals, but can account simultaneously for hydrodynamic cotransport in the presence of changes in fluorescence quantum yield. We believe this will be useful when studying interacting systems exhibiting fluorescence quenching, enhancement, or Förster resonance energy transfer with transport methods.
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Affiliation(s)
- Sumit K Chaturvedi
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland
| | - Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland.
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141
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Zhao H, Boyd LF, Schuck P. Measuring Protein Interactions by Optical Biosensors. ACTA ACUST UNITED AC 2017; 88:20.2.1-20.2.25. [PMID: 28369667 DOI: 10.1002/cpps.31] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This unit gives an introduction to the basic techniques of optical biosensing for measuring equilibrium and kinetics of reversible protein interactions. Emphasis is placed on description of robust approaches that will provide reliable results with few assumptions. How to avoid the most commonly encountered problems and artifacts is also discussed. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Huaying Zhao
- National Institutes of Health, Bethesda, Maryland
| | - Lisa F Boyd
- National Institutes of Health, Bethesda, Maryland
| | - Peter Schuck
- National Institutes of Health, Bethesda, Maryland
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142
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Lee CY, Lin CC, Liu YL, Liu GY, Liu JH, Hung HC. Molecular Interplay between the Dimer Interface and the Substrate-Binding Site of Human Peptidylarginine Deiminase 4. Sci Rep 2017; 7:42662. [PMID: 28209966 PMCID: PMC5314407 DOI: 10.1038/srep42662] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 01/13/2017] [Indexed: 02/06/2023] Open
Abstract
Our previous studies suggest that the fully active form of Peptidylarginine deiminase 4 (PAD4) should be a dimer and not a monomer. This paper provides a plausible mechanism for the control of PAD4 catalysis by molecular interplay between its dimer-interface loop (I-loop) and its substrate-binding loop (S-loop). Mutagenesis studies revealed that two hydrophobic residues, W347 and V469, are critical for substrate binding at the active site; mutating these two residues led to a severe reduction in the catalytic activity. We also identified several hydrophobic amino acid residues (L6, L279 and V283) at the dimer interface. Ultracentrifugation analysis revealed that interruption of the hydrophobicity of this region decreases dimer formation and, consequently, enzyme activity. Molecular dynamic simulations and mutagenesis studies suggested that the dimer interface and the substrate-binding site of PAD4, which consist of the I-loop and the S-loop, respectively, are responsible for substrate binding and dimer stabilization. We identified five residues with crucial roles in PAD4 catalysis and dimerization: Y435 and R441 in the I-loop, D465 and V469 in the S-loop, and W548, which stabilizes the I-loop via van der Waals interactions with C434 and Y435. The molecular interplay between the S-loop and the I-loop is crucial for PAD4 catalysis.
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Affiliation(s)
- Chien-Yun Lee
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan.,Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | - Chu-Cheng Lin
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Yi-Liang Liu
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan.,Institute of Biochemistry, Microbiology and Immunology, Chung Shan Medical University, Taichung, Taiwan
| | - Guang-Yaw Liu
- Institute of Biochemistry, Microbiology and Immunology, Chung Shan Medical University, Taichung, Taiwan.,Division of Allergy, Immunology and Rheumatology, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Jyung-Hurng Liu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
| | - Hui-Chih Hung
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
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143
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Beattie NR, Keul ND, Sidlo AM, Wood ZA. Allostery and Hysteresis Are Coupled in Human UDP-Glucose Dehydrogenase. Biochemistry 2017; 56:202-211. [PMID: 27966912 PMCID: PMC5293408 DOI: 10.1021/acs.biochem.6b01044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human UDP-glucose dehydrogenase (hUGDH) is regulated by an atypical allosteric mechanism in which the feedback inhibitor UDP-xylose (UDP-Xyl) competes with the substrate for the active site. Binding of UDP-Xyl triggers the T131-loop/α6 allosteric switch, which converts the hexameric structure of hUGDH into an inactive, horseshoe-shaped complex (EΩ). This allosteric transition buries residue A136 in the protein core to produce a subunit interface that favors the EΩ structure. Here we use a methionine substitution to prevent the burial of A136 and trap the T131-loop/α6 switch in the active conformation. We show that hUGDHA136M does not exhibit substrate cooperativity, which is strong evidence that the methionine substitution prevents the formation of the low-UDP-Glc-affinity EΩ state. In addition, the inhibitor affinity of hUGDHA136M is reduced 14-fold, which most likely represents the Ki for competitive inhibition in the absence of the allosteric transition to the higher-affinity EΩ state. hUGDH also displays a lag in progress curves, which is caused by a slow, substrate-induced isomerization that activates the enzyme. Stopped-flow analysis shows that hUGDHA136M does not exhibit hysteresis, which suggests that the T131-loop/α6 switch is the source of the slow isomerization. This interpretation is supported by the 2.05 Å resolution crystal structure of hUGDHA136M, which shows that the A136M substitution has stabilized the active conformation of the T131-loop/α6 allosteric switch. This work shows that the T131-loop/α6 allosteric switch couples allostery and hysteresis in hUGDH.
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Affiliation(s)
- Nathaniel R. Beattie
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Nicholas D. Keul
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Andrew M. Sidlo
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Zachary A. Wood
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
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144
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Effect of arginine on oligomerization and stability of N-acetylglutamate synthase. Sci Rep 2016; 6:38711. [PMID: 27934952 PMCID: PMC5146650 DOI: 10.1038/srep38711] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 11/15/2016] [Indexed: 11/08/2022] Open
Abstract
N-acetylglutamate synthase (NAGS; E.C.2.3.1.1) catalyzes the formation of N-acetylglutamate (NAG) from acetyl coenzyme A and glutamate. In microorganisms and plants, NAG is the first intermediate of the L-arginine biosynthesis; in animals, NAG is an allosteric activator of carbamylphosphate synthetase I and III. In some bacteria bifunctional N-acetylglutamate synthase-kinase (NAGS-K) catalyzes the first two steps of L-arginine biosynthesis. L-arginine inhibits NAGS in bacteria, fungi, and plants and activates NAGS in mammals. L-arginine increased thermal stability of the NAGS-K from Maricaulis maris (MmNAGS-K) while it destabilized the NAGS-K from Xanthomonas campestris (XcNAGS-K). Analytical gel chromatography and ultracentrifugation indicated tetrameric structure of the MmMNAGS-K in the presence and absence of L-arginine and a tetramer-octamer equilibrium that shifted towards tetramers upon binding of L-arginine for the XcNAGS-K. Analytical gel chromatography of mouse NAGS (mNAGS) indicated either different oligomerization states that are in moderate to slow exchange with each other or deviation from the spherical shape of the mNAGS protein. The partition coefficient of the mNAGS increased in the presence of L-arginine suggesting smaller hydrodynamic radius due to change in either conformation or oligomerization. Different effects of L-arginine on oligomerization of NAGS may have implications for efforts to determine the three-dimensional structure of mammalian NAGS.
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145
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Rao A, Cölfen H. Mineralization and non-ideality: on nature's foundry. Biophys Rev 2016; 8:309-329. [PMID: 28510024 DOI: 10.1007/s12551-016-0228-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 09/30/2016] [Indexed: 10/20/2022] Open
Abstract
Understanding how ions, ion-clusters and particles behave in non-ideal environments is a fundamental question concerning planetary to atomic scales. For biomineralization phenomena wherein diverse inorganic and organic ingredients are present in biological media, attributing biomaterial composition and structure to the chemistry of singular additives may not provide a holistic view of the underlying mechanisms. Therefore, in this review, we specifically address the consequences of physico-chemical non-ideality on mineral formation. Influences of different forms of non-ideality such as macromolecular crowding, confinement and liquid-like organic phases on mineral nucleation and crystallization in biological environments are presented. Novel prospects for the additive-controlled nucleation and crystallization are accessible from this biophysical view. In this manner, we show that non-ideal conditions significantly affect the form, structure and composition of biogenic and biomimetic minerals.
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Affiliation(s)
- Ashit Rao
- Freiburg Institute for Advanced Studies, Albert Ludwigs University of Freiburg, 79104, Freiburg im Breisgau, Germany.
| | - Helmut Cölfen
- Physical Chemistry, Department of Chemistry, University of Konstanz, D-78457, Konstanz, Germany.
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146
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Ball NJ, Nicastro G, Dutta M, Pollard DJ, Goldstone DC, Sanz-Ramos M, Ramos A, Müllers E, Stirnnagel K, Stanke N, Lindemann D, Stoye JP, Taylor WR, Rosenthal PB, Taylor IA. Structure of a Spumaretrovirus Gag Central Domain Reveals an Ancient Retroviral Capsid. PLoS Pathog 2016; 12:e1005981. [PMID: 27829070 PMCID: PMC5102385 DOI: 10.1371/journal.ppat.1005981] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 10/06/2016] [Indexed: 12/26/2022] Open
Abstract
The Spumaretrovirinae, or foamy viruses (FVs) are complex retroviruses that infect many species of monkey and ape. Despite little sequence homology, FV and orthoretroviral Gag proteins perform equivalent functions, including genome packaging, virion assembly, trafficking and membrane targeting. However, there is a paucity of structural information for FVs and it is unclear how disparate FV and orthoretroviral Gag molecules share the same function. To probe the functional overlap of FV and orthoretroviral Gag we have determined the structure of a central region of Gag from the Prototype FV (PFV). The structure comprises two all α-helical domains NtDCEN and CtDCEN that although they have no sequence similarity, we show they share the same core fold as the N- (NtDCA) and C-terminal domains (CtDCA) of archetypal orthoretroviral capsid protein (CA). Moreover, structural comparisons with orthoretroviral CA align PFV NtDCEN and CtDCEN with NtDCA and CtDCA respectively. Further in vitro and functional virological assays reveal that residues making inter-domain NtDCEN—CtDCEN interactions are required for PFV capsid assembly and that intact capsid is required for PFV reverse transcription. These data provide the first information that relates the Gag proteins of Spuma and Orthoretrovirinae and suggests a common ancestor for both lineages containing an ancient CA fold. Foamyviruses (FVs) or Spuma-retroviruses derive their name from the cytopathic effects they cause in cell culture. However, infection in humans is benign and FVs have entered the human population through zoonosis from apes resulting in the emergence of Prototype FV (PFV). Like all retroviruses, FVs contain gag, pol and env structural genes and replicate through reverse-transcription and host genome integration. Gag, the major structural protein, is required for genome packaging, virion assembly, trafficking and egress. However, although functionally equivalent, FV and orthoretroviral Gag share little sequence homology and it is unclear how they perform the same function. Therefore, to understand more about relationship between FV and orthoretroviral replication we have carried out structural studies of PFV-Gag. Here we present the structure of CA domains from a central region PFV-Gag and show that despite little sequence similarity they share the same fold as the CA domains of orthoretroviral Gag. These data provide the first information relating the Spuma and Orthoretrovirinae Gag proteins. We discuss our findings in terms of evolutionary divergence of spuma and orthoretroviral lineages.
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Affiliation(s)
- Neil J. Ball
- Macromolecular Structure Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Giuseppe Nicastro
- Macromolecular Structure Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Moumita Dutta
- Structural Biology of Cells and Viruses, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Dominic J. Pollard
- Macromolecular Structure Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - David C. Goldstone
- Macromolecular Structure Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Marta Sanz-Ramos
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Andres Ramos
- Macromolecular Structure Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Erik Müllers
- Institute of Virology, Technische Universität Dresden, Dresden, DE
| | | | - Nicole Stanke
- Institute of Virology, Technische Universität Dresden, Dresden, DE
| | - Dirk Lindemann
- Institute of Virology, Technische Universität Dresden, Dresden, DE
| | - Jonathan P. Stoye
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
- Faculty of Medicine, Imperial College London, London, United Kingdom
| | - William R. Taylor
- Computational Cell and Molecular Biology Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Peter B. Rosenthal
- Structural Biology of Cells and Viruses, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Ian A. Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
- * E-mail:
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147
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Complex structure of the fission yeast SREBP-SCAP binding domains reveals an oligomeric organization. Cell Res 2016; 26:1197-1211. [PMID: 27811944 PMCID: PMC5099872 DOI: 10.1038/cr.2016.123] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 08/05/2016] [Accepted: 08/26/2016] [Indexed: 12/22/2022] Open
Abstract
Sterol regulatory element-binding protein (SREBP) transcription factors are master regulators of cellular lipid homeostasis in mammals and oxygen-responsive regulators of hypoxic adaptation in fungi. SREBP C-terminus binds to the WD40 domain of SREBP cleavage-activating protein (SCAP), which confers sterol regulation by controlling the ER-to-Golgi transport of the SREBP-SCAP complex and access to the activating proteases in the Golgi. Here, we biochemically and structurally show that the carboxyl terminal domains (CTD) of Sre1 and Scp1, the fission yeast SREBP and SCAP, form a functional 4:4 oligomer and Sre1-CTD forms a dimer of dimers. The crystal structure of Sre1-CTD at 3.5 Å and cryo-EM structure of the complex at 5.4 Å together with in vitro biochemical evidence elucidate three distinct regions in Sre1-CTD required for Scp1 binding, Sre1-CTD dimerization and tetrameric formation. Finally, these structurally identified domains are validated in a cellular context, demonstrating that the proper 4:4 oligomeric complex formation is required for Sre1 activation.
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148
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An Adaptive Mutation in Enterococcus faecium LiaR Associated with Antimicrobial Peptide Resistance Mimics Phosphorylation and Stabilizes LiaR in an Activated State. J Mol Biol 2016; 428:4503-4519. [PMID: 27670715 DOI: 10.1016/j.jmb.2016.09.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 08/15/2016] [Accepted: 09/20/2016] [Indexed: 11/23/2022]
Abstract
The cyclic antimicrobial lipopeptide daptomycin (DAP) triggers the LiaFSR membrane stress response pathway in enterococci and many other Gram-positive organisms. LiaR is the response regulator that, upon phosphorylation, binds in a sequence-specific manner to DNA to regulate transcription in response to membrane stress. In clinical settings, non-susceptibility to DAP by Enterococcus faecium is correlated frequently with a mutation in LiaR of Trp73 to Cys (LiaRW73C). We have determined the structure of the activated E. faecium LiaR protein at 3.2Å resolution and, in combination with solution studies, show that the activation of LiaR induces the formation of a LiaR dimer that increases LiaR affinity at least 40-fold for the extended regulatory regions upstream of the liaFSR and liaXYZ operons. In vitro, LiaRW73C induces phosphorylation-independent dimerization of LiaR and provides a biochemical basis for non-susceptibility to DAP by the upregulation of the LiaFSR regulon. A comparison of the E. faecalis LiaR, E. faecium LiaR, and the LiaR homolog from Staphylococcus aureus (VraR) and the mutations associated with DAP resistance suggests that physicochemical properties such as oligomerization state and DNA specificity, although tuned to the biology of each organism, share some features that could be targeted for new antimicrobials.
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149
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The Crystal Structure of Peroxiredoxin Asp f3 Provides Mechanistic Insight into Oxidative Stress Resistance and Virulence of Aspergillus fumigatus. Sci Rep 2016; 6:33396. [PMID: 27624005 PMCID: PMC5022050 DOI: 10.1038/srep33396] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 08/03/2016] [Indexed: 12/22/2022] Open
Abstract
Invasive aspergillosis and other fungal infections occur in immunocompromised individuals, including patients who received blood-building stem cell transplants, patients with chronic granulomatous disease (CGD), and others. Production of reactive oxygen species (ROS) by immune cells, which incidentally is defective in CGD patients, is considered to be a fundamental process in inflammation and antifungal immune response. Here we show that the peroxiredoxin Asp f3 of Aspergillus fumigatus inactivates ROS. We report the crystal structure and the catalytic mechanism of Asp f3, a two-cysteine type peroxiredoxin. The latter exhibits a thioredoxin fold and a homodimeric structure with two intermolecular disulfide bonds in its oxidized state. Replacement of the Asp f3 cysteines with serine residues retained its dimeric structure, but diminished Asp f3's peroxidase activity, and extended the alpha-helix with the former peroxidatic cysteine residue C61 by six residues. The asp f3 deletion mutant was sensitive to ROS, and this phenotype was rescued by ectopic expression of Asp f3. Furthermore, we showed that deletion of asp f3 rendered A. fumigatus avirulent in a mouse model of pulmonary aspergillosis. The conserved expression of Asp f3 homologs in medically relevant molds and yeasts prompts future evaluation of Asp f3 as a potential therapeutic target.
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150
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Liu YC, Lee CY, Lin CL, Chen HY, Liu GY, Hung HC. Multifaceted interactions and regulation between antizyme and its interacting proteins cyclin D1, ornithine decarboxylase and antizyme inhibitor. Oncotarget 2016; 6:23917-29. [PMID: 26172301 PMCID: PMC4695161 DOI: 10.18632/oncotarget.4469] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 06/16/2015] [Indexed: 11/25/2022] Open
Abstract
Ornithine decarboxylase (ODC), cyclin D1 (CCND1) and antizyme inhibitor (AZI) promote cell growth. ODC and CCND1 can be degraded through antizyme (AZ)-mediated 26S proteasomal degradation. This paper describes a mechanistic study of the molecular interactions between AZ and its interacting proteins. The dissociation constant (Kd) of the binary AZ-CCND1 complex and the respective binding sites of AZ and CCND1 were determined. Our data indicate that CCND1 has a 4-fold lower binding affinity for AZ than does ODC and an approximately 40-fold lower binding affinity for AZ than does AZI. The Kd values of AZ-CCND1, AZ-ODC and AZ-AZI were 0.81, 0.21 and 0.02 μM, respectively. Furthermore, the Kd values for CCND1 binding to the AZ N-terminal peptide (AZ34–124) and AZ C-terminal peptide (AZ100–228) were 0.92 and 8.97 μM, respectively, indicating that the binding site of CCND1 may reside at the N-terminus of AZ, rather than the C-terminus. Our data also show that the ODC-AZ-CCND1 ternary complex may exist in equilibrium. The Kd values of the [AZ-CCND1]-ODC and [AZ-ODC]-CCND1 complexes were 1.26 and 4.93 μM, respectively. This is the first paper to report the reciprocal regulation of CCND1 and ODC through AZ-dependent 26S proteasomal degradation.
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Affiliation(s)
- Yen-Chin Liu
- Department of Life Sciences, National Chung Hsing University (NCHU), Taichung, Taiwan
| | - Chien-Yun Lee
- Department of Life Sciences, National Chung Hsing University (NCHU), Taichung, Taiwan.,Graduate Institute of Biotechnology, National Chung-Hsing University (NCHU), Taichung, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | - Chi-Li Lin
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Hui-Yi Chen
- Biotechnology Center, National Chung-Hsing University (NCHU), Taichung, Taiwan.,Agricultural Biotechnology Center (ABC), National Chung-Hsing University (NCHU), Taichung, Taiwan
| | - Guang-Yaw Liu
- Institute of Microbiology & Immunology, Chung Shan Medical University, Taichung, Taiwan.,Division of Allergy, Immunology, and Rheumatology, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Hui-Chih Hung
- Department of Life Sciences, National Chung Hsing University (NCHU), Taichung, Taiwan.,Agricultural Biotechnology Center (ABC), National Chung-Hsing University (NCHU), Taichung, Taiwan.,Institute of Genomics and Bioinformatics, National Chung Hsing University (NCHU), Taichung, Taiwan
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